diff --git a/packages/engine/src/__tests__/self-healing.test.ts b/packages/engine/src/__tests__/self-healing.test.ts
index 1431a9ed3..ea00a7ad4 100644
--- a/packages/engine/src/__tests__/self-healing.test.ts
+++ b/packages/engine/src/__tests__/self-healing.test.ts
@@ -1024,6 +1024,31 @@ describe("SelfHealingManager", () => {
 
       managerWithRecovery.stop();
     });
+
+    it("does not clear errors on paused tasks (respects user investigate intent)", async () => {
+      const managerWithRecovery = new SelfHealingManager(store, {
+        rootDir: "/tmp/test-project",
+      });
+
+      (store.listTasks as ReturnType<typeof vi.fn>).mockResolvedValue([
+        {
+          id: "FN-303",
+          column: "in-review",
+          status: "failed",
+          paused: true,
+          error: "Agent finished without calling task_done",
+          steps: [{ status: "done" }, { status: "done" }],
+          log: [],
+        },
+      ]);
+
+      const result = await managerWithRecovery.recoverMisclassifiedFailures();
+
+      expect(result).toBe(0);
+      expect(store.updateTask).not.toHaveBeenCalled();
+
+      managerWithRecovery.stop();
+    });
   });
 
   describe("recoverPartialProgressNoTaskDoneFailures", () => {
@@ -1642,6 +1667,33 @@ describe("SelfHealingManager", () => {
 
       managerWithRecovery.stop();
     });
+
+    it("does not move paused merged tasks to done (respects user pause intent)", async () => {
+      const managerWithRecovery = new SelfHealingManager(store, {
+        rootDir: "/tmp/test-project",
+      });
+
+      (store.listTasks as ReturnType<typeof vi.fn>).mockResolvedValue([
+        {
+          id: "FN-352",
+          column: "in-review",
+          paused: true,
+          mergeDetails: {
+            mergeConfirmed: true,
+            mergedAt: "2026-01-01T00:00:00.000Z",
+          },
+          log: [],
+        },
+      ]);
+
+      const result = await managerWithRecovery.recoverMergedReviewTasks();
+
+      expect(result).toBe(0);
+      expect(store.updateTask).not.toHaveBeenCalled();
+      expect(store.moveTask).not.toHaveBeenCalled();
+
+      managerWithRecovery.stop();
+    });
   });
 
   describe("recoverReviewTasksWithFailedPreMergeSteps", () => {
diff --git a/packages/engine/src/self-healing.ts b/packages/engine/src/self-healing.ts
index 5ae8ded19..665f23612 100644
--- a/packages/engine/src/self-healing.ts
+++ b/packages/engine/src/self-healing.ts
@@ -1016,6 +1016,7 @@ export class SelfHealingManager {
 
       const mergedButNotDone = tasks.filter((t) =>
         t.column === "in-review" &&
+        !t.paused &&
         t.mergeDetails?.mergeConfirmed === true,
       );
 
@@ -1069,6 +1070,7 @@ export class SelfHealingManager {
 
       const misclassified = tasks.filter((t) =>
         t.column === "in-review" &&
+        !t.paused &&
         t.status === "failed" &&
         t.error?.includes("without calling task_done") &&
         t.steps.length > 0 &&